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SOAPdenovo-Trans specifications

Information


Unique identifier OMICS_01324
Name SOAPdenovo-Trans
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yinlong Xie <>

Publication for SOAPdenovo-Trans

SOAPdenovo-Trans in pipelines

 (12)
2018
PMCID: 5818608
PMID: 29459752
DOI: 10.1038/s41598-018-21190-7

[…] and viral factors. additional pipelines for analyzing the host splicing patterns may help us to understand the virus-host interaction and co-evolution in the future., raw reads were assembled using soapdenovo-trans with the following settings: “-k 31 –i 20 -e 3 –m 3 –l 100”. we then searched for matches against a customized virus database (described below) using the basic local alignment search […]

2017
PMCID: 5435178
PMID: 28520756
DOI: 10.1371/journal.pone.0176677

[…] read archive (sra no. srp077042). after removal of adaptor sequences and low-quality reads, we obtained 25.53 gb of clean data. subsequently, these clean data were assembled into 105,127 unigenes by soapdenovo-trans []. lengths of the unigenes ranged from 150 to 34,811 nt, with an average length of 682 nt and the n50 size of 1,257 nt ()., to predict the function classification and annotation […]

2016
PMCID: 5020319
PMID: 27618997
DOI: 10.1038/srep28199

[…] of in silico reads using a perl script housed in the trinity software package, the reduced reads were assembled following the steps described in , using three different assemblers: trinity, soapdenovo-trans, and velvet. the consensus set of unigenes of the three different methods was used as the final representative transcriptome assembly, which resulted in 89,754 unigenes with a n50 […]

2016
PMCID: 5112563
PMID: 27853259
DOI: 10.1038/srep37244

[…] with 72 bases length using casava 1.8 package tool provided by illumina. reads’ quality was assessed using filter tool. high quality reads were used for de novo assembly till scaffold level using soapdenovo-trans tool for three tea cultivars separately. k-mer size of 61 was selected for each of the assembly as it achieved the best balance between the numbers of transcripts produced, average […]

2016
PMCID: 5123303
PMID: 28105944
DOI: 10.1186/s12870-016-0927-9

[…] (agilent technologies, usa), then libraries were sequenced on illumina gaiix platform. raw reads were trimmed and filtered with trimmomatic []. the assembly of transcriptome was performed using soapdenovo-trans transcriptome assembler. assembled transcripts were mapped to l. usitatissimum ‘reference’ transcriptome database of jgi genome portal with blastn (phytozomev11: […]


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SOAPdenovo-Trans in publications

 (115)
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] performed using read quality filtering tool, filter in which poor quality reads and adapter contaminated reads were filtered-out. de novo assembly of good quality reads was performed using assembler soapdenovo-trans (http://soap.genomics.org.cn) which was run on different k-mer sizes ranging from 19–71 based on good quality read sequences and corresponding contigs/scaffolds were produced […]

PMCID: 5954267
PMID: 29764375
DOI: 10.1186/s12864-018-4463-x

[…] of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome., to improve the assembly quality, three computational tools (trinity, oases and soapdenovo-trans) were employed to enhance individual transcriptome assembly, and cap3 and cd-hit-est software were then used to merge these three assembled transcriptomes. in addition, functional […]

PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] shotgun assembly (tsa) database. additionally, transcripts of rhagophthalmus sp., chauliognathus flavipes and phrixothrix hirtus were downloaded from the sra archive and assembled using soapdenovo-trans-31mer 1.04 []. lantern and body transcripts of p. hirtus were merged into a single dataset (additional file : table s4) []. raw data were first examined in fastqc […]

PMCID: 5930835
PMID: 29743927
DOI: 10.1186/s12983-018-0252-2

[…] ambiguous bases (ns) or more than 50 low quality bases []. transcriptome assembly from the remaining reads followed the de bruijn graph algorithm as detailed in misof et al. [] by using the software soapdenovo-trans-31 kmer version 1.01 []. furthermore, the assembly was cleaned from remaining linker/adapter and foreign contaminations, such as vector, phage or bacterial sequences by checking […]

PMCID: 5919021
PMID: 29652888
DOI: 10.1371/journal.pntd.0006410

[…] information (ncbi) under accession srp071001 of bioproject prjna312361 and biosample samn04497582., assembly of all reads was done as described previously using the assemblers abyss and soapdenovo-trans with every kmer ending in 1 and 5 (-k program switch) from 21 to 95 [–]. resulting contigs were re-assembled by a pipeline of blastn and cap3 assembler [] as described earlier []. […]


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SOAPdenovo-Trans institution(s)
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China; BGI-Shenzhen, Shenzhen, China; HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong; Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha, China; BGI-tech, BGI-Shenzhen, Shenzhen, China; Department of Medicine, University of Alberta, Edmonton, Canada; Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Department of Biological Sciences, University of Alberta, Edmonton, Canada; The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Department of Biology, University of Copenhagen, Copenhagen, Denmark;Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
SOAPdenovo-Trans funding source(s)
Supported by The State Key Development Program for Basic Research of China-973 Program (NO.2011CB809202), Shenzhen Key Laboratory of Transomics Biotechnologies (CXB201108250096A), China National GeneBank and the 1000 plants (1KP) initiative.

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